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Crop improvement is achieved by selecting plants with favorable phenotypes. A marker can be defined as a measurable trait whose expression is highly correlated with the expression of a second trait, for which selection is carried out. Markers can be used to (i) determine the genetic diversity in germplasm and its changes over time, (ii) detect genetic relationships among germplasm in seed banks and applied breeding programs, (iii) predict heterosis and hybrid performance, (iv) map quantitative trait loci (QTL), (v) perform marker-assisted selection (MAS), and (vi) perform genomic selection. Marker technologies have a substantial impact on the methodology of plant breeding. Today, new “omics” technologies provide high throughput methods to assess DNA, RNA, proteins, and metabolites. This article will give a short overview of concepts integrating data from transcriptomics, proteomics, and metabolomics as so called “non-DNA” markers into plant breeding.
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